Bay Area Catholic colleges are joining schools nationwide to fight a federal law requiring new health plans to cover birth control, saying the rule violates their right to oppose contraception.

Dozens of schools and organizations have opposed the provision in the federal Affordable Care Act. The law, which would take effect Aug. 1, 2012, exempts some churches from including contraceptive coverage in the health care plans they offer, but not colleges or other religious groups.

Several Bay Area colleges — including Saint Mary’s College, the University of San Francisco and Santa Clara University — wrote letters of opposition to the U.S. Health and Human Services Department before a comment period on the law ended Sept. 30. Their resistance comes despite the fact they are required by California law to cover contraception for employees, and sometimes students.

Still, the federal law — which is opposed by the 200-member Association of Catholic Colleges and Universities — highlights a modern challenge for faith-based institutions.

The new federal rule would put Catholic schools in an impossible situation, Saint Mary’s College President Brother Ronald Gallagher wrote in his Aug. 31 letter expressing “deep concern” with the law.

“As the document is currently written, Catholic colleges and universities must either pay for contraception and sterilization … in violation of the church’s moral teaching,” Gallagher wrote, “or terminate those health care plans, in violation of the church’s social teaching.”

The law mostly would affect college employees, since students often are covered by their parents’ health insurance.

Most of the debate has centered on the religious exemption, which essentially eases the requirement for churches only and is nearly identical to an exemption in a California law that also requires contraception coverage. The California Supreme Court in 2004 upheld the state law, which had been challenged by a Catholic organization.

The problem, schools argue, is that the exemption is too narrowly written to include Catholic colleges, which employ and enroll a high percentage of non-Catholics. Although California institutions — and those in 27 other states that require contraception coverage — have been forced to abide by the requirement for years, the federal government should back off its plan, said Tom Poundstone, a Saint Mary’s professor of theology and religious studies.

“Why deliberately pick a fight with Catholic colleges?” he said. “The idea of compelling us to pay for services we’re opposed to is a tough thing. In crass political terms, the idea of alienating the Catholic constituency is unnecessarily divisive.”

Despite the flurry of letters to Washington, D.C., Bay Area college leaders were tight-lipped about the issue. Several colleges, such as Oakland’s Holy Names University, declined to answer questions about whether they cover contraception in student and employee health plans.

Meanwhile, many colleges have been going against the Vatican’s wishes by insuring birth control for employees and students.

Two schools with Catholic roots, Notre Dame de Namur University in Belmont and Dominican University in San Rafael, have broken somewhat from their religious identities and no longer oppose birth control.

“Catholic schools just don’t operate the way they did in the ’50s, ’60s or even the ’70s,” said Richard Rossi, a Notre Dame de Namur spokesman. “It’s the reality of the 21st century.”

Catholics nationwide are anything but united against birth control, according to an April report by the nonprofit Guttmacher Institute, a reproductive-health organization. Some 98 percent of Catholic women polled by the institute said they had used contraception banned by the Catholic Church.

“Women spend a majority of their lives trying not to get pregnant,” said Adrienne Verrilli, a spokeswoman in Planned Parenthood’s San Francisco office. “We just believe that women need as wide access to family planning as they can get.”

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